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- PDB-6qha: Crystal Structure of Human Kallikrein 6 in complex with GSK3205388B -

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Basic information

Entry
Database: PDB / ID: 6qha
TitleCrystal Structure of Human Kallikrein 6 in complex with GSK3205388B
ComponentsKallikrein-6KLK6
KeywordsHYDROLASE / Protease / Inhibitor / Complex
Function / homology
Function and homology information


tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / secretory granule / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-J2Q / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsThorpe, J.H.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2019
Title: Kallikrein 5 inhibitors identified through structure based drug design in search for a treatment for Netherton Syndrome.
Authors: White, G.V. / Edgar, E.V. / Holmes, D.S. / Lewell, X.Q. / Liddle, J. / Polyakova, O. / Smith, K.J. / Thorpe, J.H. / Walker, A.L. / Wang, Y. / Young, R.J. / Hovnanian, A.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein-6
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5268
Polymers48,8352
Non-polymers6916
Water6,503361
1
A: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8094
Polymers24,4181
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7174
Polymers24,4181
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.660, 45.850, 90.000
Angle α, β, γ (deg.)90.00, 94.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein-6 / KLK6 / Neurosin / Protease M / SP59 / Serine protease 18 / Serine protease 9 / Zyme


Mass: 24417.695 Da / Num. of mol.: 2 / Mutation: R74G/R76Q/N132Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Chemical ChemComp-J2Q / ~{N}-(4-carbamimidoylphenyl)-3-ethoxy-2-oxidanyl-benzamide


Mass: 299.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N3O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.82→47.51 Å / Num. obs: 130100 / % possible obs: 94.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 29.48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.048 / Rrim(I) all: 0.089 / Net I/σ(I): 10.3
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7335 / CC1/2: 0.655 / Rpim(I) all: 0.512 / Rrim(I) all: 0.825 / % possible all: 75.5

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimless0.3.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LO6

1lo6


Resolution: 1.82→47.51 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2021 5.01 %RANDOM
Rwork0.213 ---
obs0.215 40346 93.5 %-
Displacement parametersBiso mean: 28.37 Å2
Baniso -1Baniso -2Baniso -3
1-3.2025 Å20 Å24.444 Å2
2---1.7166 Å20 Å2
3----1.4858 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 1.82→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 53 361 3807
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0173595HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094882HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1199SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes527HARMONIC5
X-RAY DIFFRACTIONt_it3595HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion15.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion450SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4120SEMIHARMONIC4
LS refinement shellResolution: 1.82→1.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 -4.63 %
Rwork0.4 1937 -
all0.401 2031 -
obs--64.57 %

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